Table 1.

Identification of two independent association signals for overall breast cancer risk among women of European ancestry

Single marker analysisConditional analysis
SignalSNPsPosition (hg 19)AllelesbRAFLDc (r2)OR (95% CI)dPtrenddOR (95% CI)ePtrende
All cases (48,155 cases and 43,612 controls)
1frs9790517a106,084,778T/C0.231.05 (1.03–1.08)5.44 × 10−61.04 (1.02–1.07)2.51 × 10−4
2grs77928427106,356,761A/C0.240.041.05 (1.03-1.08)4.07 × 10−61.04 (1.02–1.07)1.86 × 10−4
ER+ (28,038 cases and 43,612 controls)
1rs9790517a106,084,778T/C0.231.06 (1.03–1.09)1.20 × 10−51.05 (1.02–1.08)2.49 × 10−4
2rs77928427106,356,761A/C0.240.041.05 (1.02–1.08)1.40 × 10−41.04 (1.01–1.07)3.07 × 10−3
ER (7,786 cases and 43,612 controls)
1rs9790517a106,084,778T/C0.221.04 (0.99–1.08)0.161.02 (0.98–1.07)0.3396
2rs77928427106,356,761A/C0.240.041.05 (1.01–1.09)0.031.04 (1.00–1.09)0.0508

Abbreviation: RAF, risk allele frequency.

  • aIndex SNP.

  • bRisk/reference allele; risk alleles are shown in bold.

  • cr2 for LD with the index SNP rs9790517.

  • dAdjusted for age, study, and the first six and an additional PC for LMBC study.

  • eIncluded both top SNPs and adjusted for other top SNPs, age, study sites, and the first six and an additional PC for LMBC study.

  • fA total of 23 SNPs cannot be excluded using LR < 1/100 as candidate causal variants (see Supplementary Table S1).

  • gA total of 4 SNPs cannot be excluded using LR < 1/100 as candidate causal variants (see Supplementary Table S1)